L-glutamate catabolism in Ochrobactrum thiophenivorans DSM 7216

GapMind for catabolism of small carbon sources

L-glutamate catabolism in Ochrobactrum thiophenivorans DSM 7216

Best path

Rules

Overview: Glutamate is a single transamination reaction from 2-oxoglutarate (alpha-ketoglutarate), which is an intermediate in the TCA cycle. Amino acid transaminases are often non-specific, so glutamate catabolism could be considered trivial. However, many amino acid transaminases are 2-oxoglutarate dependent, so they cannot contribute to glutamate catabolism. And even if the amino group is transfered elsewhere, the ammonium group still needs to be liberated somehow. GapMind represents glutamate degradation using MetaCyc pathways L-glutamate degradation I (glutamate dehydrogenase, link), pathway II via aspartate ammonia-lyase (link), and pathway VI via glutamate mutase (link). Several other MetaCyc pathways are not included in GapMind. Pathway IV (via gamma-aminobutanoate, link) is not thought to occur in prokaryotes. Pathways V (via hydroxyglutarate, link) and XI (reductive Stickland reaction, link) combine glutamate dehydrogenase with reductive pathways; these are omitted because glutamate dehydrogenase alone suffices for catabolism under respiratory conditions. Pathways VII (to butanoate, link) and VIII (to propanoate, link) are similar to pathway VI but also describe the fermentation of the pyruvate. Pathway IX (via 4-aminobutanoate, link) does not yield net consumption of glutamate: the catabolism of 4-aminobutanoate relies on a transamination reaction that converts 2-oxoglutarate to glutamate.

all:

glutamate-transport and gdhA
or glutamate-transport and aspA
or glutamate-transport, glmS, glmE, mal, fumD and mcl
Comment: GdhA is glutamate dehydrogenase (forming 2-oxoglutarate and ammonia). In pathway II, glutamate and oxaloacetate are transaminated to 2-oxoglutarate and aspartate, and the aspartate is cleaved to fumarate and ammonium by aspA. (The transamination reaction is not represented. Both oxaloacetate and fumarate are TCA cycle intermediates.) In pathway VI, the mutase glmSE converts glutamate to (2S,3S)-3-methylaspartate, the lyase mal forms 2-methylfumarate (mesaconate), the hydratase fumD forms (S)-2-methylmalate (citramalate), and a lyase forms acetate and pyruvate.

glutamate-transport:

gltI, gltJ, gltK and gltL
or gltL, gluB, gluC and gluD
or bztA, bztB, bztC and gltL
or braC, braD, braE, braF and braG
or gltL and glnP
or peb1A, peb1B and gltL
or gtrA, gtrB and gtrC
or aapJ, aapQ, aapM and aapP
or gltS
or acaP
or gltP
or yveA
or gltS_Syn
or dmeA
Comment: Transporters were identified using query: transporter:glutamate:L-glutamate:glu

38 steps (25 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
braC	ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC	CEV31_RS03660	CEV31_RS03655
braD	ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD)	CEV31_RS03685	CEV31_RS13110
braE	ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE)	CEV31_RS03680	CEV31_RS13105
braF	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF)	CEV31_RS03675	CEV31_RS14825
braG	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG)	CEV31_RS03670	CEV31_RS14820
gdhA	glutamate dehydrogenase, NAD-dependent	CEV31_RS03830	CEV31_RS06715
Alternative steps:
aapJ	ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ	CEV31_RS09895
aapM	ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM)	CEV31_RS09905	CEV31_RS08815
aapP	ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP	CEV31_RS09910	CEV31_RS19030
aapQ	ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)	CEV31_RS09900	CEV31_RS19045
acaP	L-glutamate permease AcaP
aspA	L-aspartate ammonia-lyase	CEV31_RS19845
bztA	L-glutamate ABC transporter, substrate-binding component	CEV31_RS09895
bztB	L-glutamate ABC transporter, permease component 1 (BztB)	CEV31_RS09900
bztC	L-glutamate ABC transporter, permease component 2 (BztC)	CEV31_RS09905
dmeA	L-glutamate transporter DmeA
fumD	(S)-2-methylmalate dehydratase (mesaconase)	CEV31_RS11230
glmE	L-glutamate mutase, E component
glmS	L-glutamate mutase, S component
glnP	L-glutamate ABC transporter, fused permease and substrate-binding components GlnP
gltI	L-glutamate ABC transporter, substrate-binding component (GltI/AatJ)	CEV31_RS09375
gltJ	L-glutamate ABC transporter, permease component 1 (gltJ/aatQ)	CEV31_RS19045	CEV31_RS19200
gltK	L-glutamate ABC transporter, permease component 1 (gltK/aatM)	CEV31_RS19045	CEV31_RS13485
gltL	L-glutamate ABC transporter, ATPase component (GltL/GluA/BztD/GlnQ/AatP/PEB1C)	CEV31_RS09910	CEV31_RS19030
gltP	L-glutamate:cation symporter GltP/GltT	CEV31_RS14880
gltS	L-glutamate:Na+ symporter GltS
gltS_Syn	L-glutamate:Na+ symporter GltS_Syn
gluB	L-glutamate ABC transporter, substrate-binding component GluB
gluC	L-glutamate ABC transporter, permease component 1 (GluC)	CEV31_RS13545	CEV31_RS18520
gluD	L-glutamate ABC transporter, permease component 2 (GluD)	CEV31_RS19065	CEV31_RS17385
gtrA	tripartite L-glutamate:Na+ symporter, small membrane component GtrA
gtrB	tripartite L-glutamate:Na+ symporter, large membrane component GtrB
gtrC	tripartite L-glutamate:Na+ symporter, substrate-binding component GtrC
mal	methylaspartate ammonia-lyase
mcl	(S)-citramalyl-CoA pyruvate-lyase	CEV31_RS16930	CEV31_RS17160
peb1A	L-glutamate ABC transporter, substrate-binding component Peb1A	CEV31_RS01760
peb1B	L-glutamate ABC transporter, permease component Peb1B	CEV31_RS17385	CEV31_RS20530
yveA	L-glutamate:H+ symporter YveA

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources